Brachiopods are sessile bivalved spiralians closely related to annelids, molluscs, and nemerteans. Despite having an unsegmented adult body, the larval body of many brachiopods is divided in lobes disposed along the anterior-posterior axis. This morphology and presence of partitioned coeloms in some larvae have been treated as evidence that brachiopods evolved from a segmented ancestor. We approached this hypothesis by characterizing the development of brachiopod larval lobes and the expression of genes commonly expressed in segments of arthropods and annelids (i.e. "segment polarity" genes) in the trilobed larva of Terebratalia transversa and the bilobed larva of Novocrania anomala. We have cloned Engrailed, Wnt genes, and components of the Hedgehog pathway and analysed their expression by in situ hybridization. The three lobes of T. transversa larva were delimited by an anterior ectodermal groove and a posterior less prominent constriction. We detected adjacent stripes of wnt1 and engrailed transcripts in the ectoderm delimiting the anterior boundary. At the posterior boundary, wnt1 and engrailed were co-expressed on a ventral and a dorsal band. Genes of the Hedgehog pathway were not expressed on the larval lobes. Adjacent stripes of wnt1 and engrailed are also found at parasegment and segment boundaries of arthropods and annelids, respectively, while co-expression is observed in the chordate mid-hindbrain boundary and hemichordate collar-trunk boundary. Thus, our results suggest that engrailed and wnt1, but not hedgehog, might be involved in the development of lobe boundaries of T. transversa larvae in a similar manner as observed in other morphological boundaries.